Browsing by Subject "microbiology"
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Item ELUCIDATING THE DIVERSITY OF MICROBIAL RETTING COMMUNITIES ON HIBISCUS CANNABINUS USING NEXT-GENERATION SEQUENCING(2014-03) Visi, David K.; Allen, Michael S.Purpose (a): Global environmental concerns have led to a growing interest in renewable resources such as plant-based fibers. Beyond textiles and cordage, plant fibers have the potential for incorporation into renewable, bio-based composite materials for the building and manufacturing sectors. Successful commercialization of fiber production requires optimization of fiber extraction. Retting is the traditional method of fiber extraction, whereby endogenous microorganisms break down heteropolysaccharides to release fiber bundles. Previous studies have analyzed the retting solution for its bacterial constituents, but none have followed changes in the microbial community through the retting process. This research aims to track the bacterial components of the retting community through time, and determine the effects of bacterial augmentation with isolated pectinolytic bacteria using next generation sequencing of 16S rRNA gene amplicons. Methods (b): Batch C1 included plant material and an inoculum of pond water represented a “traditional” retting environment, while C2 contained autoclaved pond water to represent the endogenous microorganisms associated with the plant material. Experimental batch E1 included the addition of three pectinolytic bacterial isolates: Bacillus DP1, Paenibacillus DP2, and Bacillus K1. Total DNA was extracted from the surface-adhering biofilm bacteria and used for PCR with full-length 16S primers 27F and 1492R. Amplification products were used as templates for a nested PCR with primers 786F and 939R targeting variable region 5 of the 16S molecule. The nested 16S rRNA amplicons were then sequenced on the next-generation Ion Torrent PGM platform. Results (c): The E1 environment showed a marked increase in phylum Firmicutes (55 to 94%), while phylum Proteobacteria showed a progressive decrease from Day 1 to 4 (36% to 5%). This was correlated with easy separation of fibers by mechanical movement. At a finer taxonomic level, E1 showed a rapid loss of inoculated Bacillus species DP1 and K1, and a more gradual loss of the family Paenibacillaceae 1 (P. DP2) as the time course progressed. In contrast, C1 was co-dominated by phyla Firmicutes and Proteobacteria, while C2 was composed in large part by the phylum Bacteroidetes. Additionally, comparison of the microbial communities under the different conditions revealed differences in diversity and composition at day 4 time points between the three conditions. Conclusions (d): Introduction of pectinolytic bacteria into the batch reactions increased production rate and increased fiber quality. Introduction of Paenibacillus DP2 is likely the driving force behind the community shifts detected in E1, which warrants further study to determine the mechanism of action. The findings confirmed previous studies that suggest a gradual replacement of aerobic organisms to an environment that is dominated by strict anaerobes. Moreover, the efforts shed light on conditions and mechanisms for the manipulation of microbiomes. These approaches may have relevance to the treatment of dysbiosis in the gut flora in humans and the treatment of related diseases.Item Harris, Elizabeth, Ph.D.(1980-01-01) Harris, Elizabeth; Stokes, C. RayThe first faculty member to be employed by TCOM, Dr. Harris was associate professor and for many years chairman of the microbiology and immunology department. She shares her teaching experiences at the college from its beginnings on the fifth floor of the Fort Worth Osteopathic Hospital on October 1, 1970, to the present state-of-the-art facilities provided in Medical Education Building 2. Interviewed by C. Ray Stokes, November 19 and December 17, 1980Item Identification of Novel Genes Involved in Escherichia coli Biofilm Formation(2003-05-01) DesPlas, Rebecca L.; Jerry Simecka; Ming-Chi WuDesPlas, Rebecca L., Identification of Novel Genes Involved in Escherichia coli Biofilm Formation. Master of Science (Microbiology), May 2003, 77 pp., 6 tables, 11 figures, references, 55 titles. Transposon mutagenesis using a miniTn10::camR transposon generated 800 random insertion mutants displaying altered biofilm phenotypes as compared to the parent strain, TRMG F/M. Transduction of the resistance marker confirmed approximately 150 biofilm mutants. Amplifications of the insertion sites, nucleotide sequencing and BLAST searches against E. coli K-12 genomic databases, identified118 of these sites. Many of the interrupted genes are not known to be associated with biofilm formation. Four mutations were transduced into E. coli K-12 MG1655, creating altered biofilm phenotypes. A plasmid clone of the nhaAR operon complemented the corresponding mutations. Results indicate that the genes identified in this study influence biofilm formation. However, further studies are needed to determine the degree of impact in a wild type strain background.Item The Picture of C. difficile epidemic and non-epidemic ribotypes: are there differences in virulence?(2019-12) Vitucci, John C.; Simecka, Jerry W.; Hodge, Lisa M.; Allen, Michael S.; Hurdle, Julian; Sumien, NathalieThe purpose of these studies was to determine if the epidemic ribotype of C. difficile (now Clostridioides difficile) was more virulent than non-epidemic ribotypes, to ascertain whether clinics contribute to community-acquired C. difficile, and to bridge gaps in understanding between C. difficile epidemiology and pathology. Virulence of the epidemic isolates was determined to be greater than non-epidemic isolates within LD50 studies utilizing a hamster model of C. difficile disease. In the epidemic isolates, increased production of toxins A and B, increased spore adherence ability, and increased production of spores when antibiotic treatment was administered were factors that are believed to play a role both in increased virulence and in the ability of the epidemic isolate to persist as epidemic. Our results indicate that primary care clinics have higher frequency of contamination of C. difficile spores than hospitals. The study also revealed that of all the samples positive for C. difficile, approximately 90% contained the genes for toxins A, B or both. Thus, primary care clinics can be a source of C. difficile and contribute to community-acquired C. difficile. However, the epidemic ribotype of C. difficile was not isolated at significantly increased levels compared to non-epidemic ribotypes. This suggests that other factors may contribute to its increased frequency of C. difficile infection diagnosis. Isolates of the epidemic ribotype were found to be more virulent than other non-epidemic isolates in both the hamster and mouse models of CDI. In particular, the epidemic ribotypes of C. difficile had lower LD50 values in hamsters than the non-epidemic isolates. The increased severity of disease was associated with higher levels of toxins A and B, but not the number of organisms recovered. The increased toxin production was observed in both the hamster and mouse models of CDI. In addition, it is believed that increased ability of epidemic isolate spores to adhere to the intestinal epithelium in vitro, and produce more spores when treated with the antibiotic vancomycin in hamsters are also important contributors to the enhanced virulence and prevalence associated with epidemic isolates of C. difficile. This revealed a possible link between C. difficile's epidemiology and pathology, and suggested that this connection can potentially explain how epidemic ribotypes persist as epidemic. Though it is likely that the factors discussed throughout this dissertation play a significant role in the epidemic ribotype's ability to persist as epidemic, it is important to note that there may be other contributing factors, such as those found in the in vivo environment. These other factors should be accounted for during future studies of C. difficile's virulence, as future ribotypes are characterized, and as novel treatments are developed to combat C. difficile infections. Still, it is strongly believed that the findings in this dissertation contribute significantly to understanding why the epidemic ribotype is epidemic, and to exposing virulence characteristics that are contributing to this.